if ( defined( 'BP_ENABLE_MULTIBLOG' ) || 1 != BP_ROOT_BLOG) {
/* If we are running BuddyPress on any blog, or not on the root blog, we need to first
shift off the blog name if we are running a subdirectory install of WPMU. */
if ( $current_blog->path != '/' )
array_shift( $bp_uri );
}

should I just add that code as it is to the top of bp-core.php?

I tried doing that but did not see any changes. I am guessing there must be more involved in the fix